Sodium in PDB 4qwx: Ycp in Complex with the Epoxyketone Inhibitor Onx 0914

All present enzymatic activity of Ycp in Complex with the Epoxyketone Inhibitor Onx 0914:
3.4.25.1;

The structure of Ycp in Complex with the Epoxyketone Inhibitor Onx 0914, PDB code: 4qwx was solved by E.M.Huber, W.Heinemeyer, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	135.600, 300.050, 145.620, 90.00, 112.77, 90.00
R / Rfree (%)	17.2 / 21.2

The structure of Ycp in Complex with the Epoxyketone Inhibitor Onx 0914 also contains other interesting chemical elements:

Magnesium	(Mg)	8 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Ycp in Complex with the Epoxyketone Inhibitor Onx 0914 (pdb code 4qwx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Ycp in Complex with the Epoxyketone Inhibitor Onx 0914, PDB code: 4qwx:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Ycp in Complex with the Epoxyketone Inhibitor Onx 0914


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ycp in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range: probe atom residue distance (Å) B Occ K:Na303 b:32.5 occ:1.00 O13 K:04C301 3.2 49.1 1.0 OG1 K:THR21 3.6 58.9 1.0 C12 K:04C301 3.7 37.2 1.0 CG K:TYR170 4.1 54.3 1.0 CB K:TYR170 4.3 54.4 1.0 CD2 K:TYR170 4.3 52.5 1.0 C40 K:04C301 4.4 46.5 1.0 CD1 K:TYR170 4.4 55.1 1.0 O2S K:MES304 4.4 58.8 1.0 CB K:THR21 4.7 60.2 1.0 O1S K:MES304 4.8 53.6 1.0 CE2 K:TYR170 4.8 51.5 1.0 CE1 K:TYR170 4.9 51.6 1.0 C41 K:04C301 4.9 48.0 1.0

Sodium binding site 2 out of 2 in the Ycp in Complex with the Epoxyketone Inhibitor Onx 0914


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ycp in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range: probe atom residue distance (Å) B Occ Y:Na303 b:24.9 occ:1.00 O13 Y:04C301 3.1 37.5 1.0 C12 Y:04C301 3.5 29.7 1.0 OG1 Y:THR21 3.5 57.0 1.0 CG Y:TYR170 4.1 54.0 1.0 CB Y:TYR170 4.2 52.1 1.0 O2S Y:MES304 4.2 57.4 1.0 C40 Y:04C301 4.3 44.3 1.0 CD2 Y:TYR170 4.3 54.1 1.0 CD1 Y:TYR170 4.4 55.0 1.0 CB Y:THR21 4.7 57.3 1.0 O1S Y:MES304 4.7 51.3 1.0 CE2 Y:TYR170 4.9 53.0 1.0 C41 Y:04C301 4.9 46.4 1.0 S Y:MES304 4.9 53.2 1.0 C10 Y:04C301 5.0 29.1 1.0 CE1 Y:TYR170 5.0 53.5 1.0

E.M.Huber, W.Heinemeyer, M.Groll. Bortezomib-Resistant Mutant Proteasomes: Structural and Biochemical Evaluation with Carfilzomib and Onx 0914. Structure 2015.
ISSN: ISSN 0969-2126
PubMed: 25599643
DOI: 10.1016/J.STR.2014.11.019